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Langdon, W. B.

Publications and source records attributed to Langdon, W. B..

2 recordsLinked to original sources
bioRxiv2018

CUDA RNAfold

We add CUDA GPU C program code to RNAfold to enable both it to be run on nVidia gaming graphics hardware and so that many thousands of RNA secondary structures can be computed in parallel. RNAfold predicts the folding pattern for RNA molecules by using O(n3) dynamic programming matrices to minimise the free energy of treating them as a sequence of bases. We benchmark RNAfold on RNA STRAND and artificial sequences of upto 30 000 bases on two GPUs and a GPGPU Tesla. The speed up is variable but up to 14 times.

bioinformatics↗
bioRxiv2017

Evolving better RNAfold C source code

Grow and graft genetic programming (GGGP) can automatically evolve an existing state-of-the art program to give more accurate predictions of the secondary structures adapted by RNA molecules using their base sequence alone. That is, genetic improvement (GI) can make functional as well as non-functional source code changes.

bioinformatics↗